MM-6mAPred: identifying DNA N6-methyladenine sites based on Markov model

• Published in: Bioinformatics Vol. 36; no. 2; pp. 388 - 392
• Main Authors: Pian, Cong, Zhang, Guangle, Li, Fei, Fan, Xiaodan
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 15.01.2020
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btz556

Abstract Motivation Recent studies have shown that DNA N6-methyladenine (6mA) plays an important role in epigenetic modification of eukaryotic organisms. It has been found that 6mA is closely related to embryonic development, stress response and so on. Developing a new algorithm to quickly and accurately identify 6mA sites in genomes is important for explore their biological functions. Results In this paper, we proposed a new classification method called MM-6mAPred based on a Markov model which makes use of the transition probability between adjacent nucleotides to identify 6mA site. The sensitivity and specificity of our method are 89.32% and 90.11%, respectively. The overall accuracy of our method is 89.72%, which is 6.59% higher than that of the previous method i6mA-Pred. It indicated that, compared with the 41 nucleotide chemical properties used by i6mA-Pred, the transition probability between adjacent nucleotides can capture more discriminant sequence information. Availability and implementation The web server of MM-6mAPred is freely accessible at http://www.insect-genome.com/MM-6mAPred/ Supplementary information Supplementary data are available at Bioinformatics online.